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Eimeria maxima phosphatidylinositol 4-phosphate 5-kinase: locus sequencing, characterization, and cross-phylum comparison

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Abstract

Phosphatidylinositol 4-phosphate 5-kinase (PIP5K) may play an important role in host-cell invasion by the Eimeria species, protozoan parasites which can cause severe intestinal disease in livestock. Here, we report the structural organization of the PIP5K gene in Eimeria maxima (Weybridge strain). Two E. maxima BAC clones carrying the E. maxima PIP5K (EmPIP5K) coding sequences were selected for shotgun sequencing, yielding a 9.1-kb genomic segment. The EmPIP5K coding region was initially identified using in silico gene-prediction approaches and subsequently confirmed by mapping rapid amplification of cDNA ends and RT-PCR-generated cDNA sequence to its genomic segment. The putative EmPIP5K gene was located at position 710-8036 nt on the complimentary strand and comprised of 23 exons. Alignment of the 1147 amino acid sequence with previously annotated PIP5K proteins from other Apicomplexa species detected three conserved motifs encompassing the kinase core domain, which has been shown by previous protein deletion studies to be necessary for PIP5K protein function. Phylogenetic analysis provided further evidence that the putative EmPIP5K protein is orthologous to that of other Apicomplexa. Subsequent comparative gene structure characterization revealed events of intron loss/gain throughout the evolution of the apicomplexan PIP5K gene. Further scrutiny of the genomic structure revealed a possible trend towards “intron gain” between two of the motif regions. Our findings offer preliminary insights into the structural variations that have occurred during the evolution of the PIP5K locus and may aid in understanding the functional role of this gene in the cellular biology of apicomplexan parasites.

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References

  • Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21(9):2104–2105

    Article  CAS  PubMed  Google Scholar 

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  PubMed  Google Scholar 

  • Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MDR (2001) InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 29:37–40

    Article  CAS  PubMed  Google Scholar 

  • Basu MK, Rogozin IB, Deusch O, Dagan T, Martin W, Koonin EV (2008) Evolutionary dynamics of introns in plastid-derived genes in plants: saturation nearly reached but slow intron gain continues. Mol Biol Evol 25:111–119

    Article  CAS  PubMed  Google Scholar 

  • Baum J, Gilberger TW, Frischknecht F, Meissner M (2008) Host-cell invasion by malaria parasites: insights from Plasmodium and Toxoplasma. Trends Parasitol 24:557–563

    Article  CAS  PubMed  Google Scholar 

  • Berman HM, Henrick K, Nakamura H (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10:980

    Article  CAS  PubMed  Google Scholar 

  • Blake DP, Smith AL, Shirley MW (2003) Amplified fragment length polymorphism analyses of Eimeria spp.: an improved process for genetic studies of recombinant parasites. Parasitol Res 90:473–475

    Article  CAS  PubMed  Google Scholar 

  • Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268:78–94

    Article  CAS  PubMed  Google Scholar 

  • Burgoyne RD, O'Callaghan DW, Hasdemir B, Haynes LP, Tepikin AV (2004) Neuronal Ca2+-sensor proteins: multitalented regulators of neuronal function. Trends Neurosci 27:203–209

    Article  CAS  PubMed  Google Scholar 

  • Caldas LA, de Souza W, Attias M (2007) Calcium ionophore-induced egress of Toxoplasma gondii shortly after host cell invasion. Vet Parasitol 147:210–220

    Article  CAS  PubMed  Google Scholar 

  • Carmel L, Wolf YI, Rogozin IB, Koonin EV (2007) Three distinct modes of intron dynamics in the evolution of Eukaryotes. Genome Res 17:1034–1044

    Article  CAS  PubMed  Google Scholar 

  • Carreno RA, Matrin DS, Barta JR (1999) Cryptosporidium is more closely related to the gregarines than to coccidia as shown by phylogenetic analysis of apicomplexan parasites inferred using small-subunit ribosomal RNA gene sequences. Parasitol Res 85:899–904

    Article  CAS  PubMed  Google Scholar 

  • Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552

    CAS  PubMed  Google Scholar 

  • Dobrowolski JM, Sibley LD (1996) Toxoplasma invasion of mammalian cells is powered by the actin cytoskeleton of the parasite. Cell 84:933–939

    Article  CAS  PubMed  Google Scholar 

  • Dobrowolski JM, Carruthers VB, Sibley LD (1997) Participation of myosin in gliding motility and host cell invasion by Toxoplasma gondii. Mol Microbiol 26:163–173

    Article  CAS  PubMed  Google Scholar 

  • Dubremetz JF, Garcia-Reguet N, Conseil V, Fourmaux MN (1998) Apical organelles and host-cell invasion by Apicomplexa. Int J Parasitol 28:1007–1013

    Article  CAS  PubMed  Google Scholar 

  • Dunn PPJ, Bumstead JM, Tomley FM (1996) Sequence, expression and localization of calmodulin-domain protein kinases in Eimeria tenella and Eimeria maxima. Parasitol 113:439–448

    Article  CAS  Google Scholar 

  • Dunn PP, Billington K, Bumstead JM, Tomley FM (1995) Isolation and sequences of cDNA clones for cytosolic and organellar hsp70 species in Eimeria spp. Mol Biochem Parasitol 70:211–215

    Article  CAS  PubMed  Google Scholar 

  • Escalante A, Ayala F (1995) Evolutionary origin of Plasmodium and other Apicomplexa based on rRNA genes. Proc Natl Acad Sci USA 92:5793–5797

    Article  CAS  PubMed  Google Scholar 

  • Gonzalez V, Combe A, David V, Malmquist NA, Delorme V, Leroy C, Blazquez S, Ménard R, Tardieux I (2009) Host cell entry by apicomplexa parasites requires actin polymerization in the host cell. Cell Host & Microbe 5:259–272

    Article  CAS  Google Scholar 

  • Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704

    Article  PubMed  Google Scholar 

  • Ishihara H, Shibasaki Y, Kizuki N, Wada T, Yazaki Y, Asano T, Oka Y (1998) Type I phosphatidylinositol-4-phosphate 5-kinases: cloning of the third isoform and deletion/substitution analysis of members of this novel lipid kinase family. J Biol Chem 273:8741–8748

    Article  CAS  PubMed  Google Scholar 

  • Jean L, Perry P, Dunn P, Bumstead J, Billington K, Ryan R, Tomley F (2001) Genomic organization and developmentally regulated expression of an apicomplexan aspartyl proteinase. Gene 262:129–136

    Article  CAS  PubMed  Google Scholar 

  • Jeffares DC, Mourier T, Penny D (2006) The biology of intron gain and loss. Trends Genet 22:16–22

    Article  CAS  PubMed  Google Scholar 

  • Katinka MD, Duprat S, Cornillot E, Metenier G, Thomarat F, Prensier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, Delbac F, Alaoui HE, Peyret P, Saurin W, Gouy M, Weissenbach J, Vivares CP (2001) Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414:450–453

    Article  CAS  PubMed  Google Scholar 

  • Kelley LA, Sternberg MJE (2009) Protein structure prediction on the web: a case study using the Phyre server. Nat Protocol 4:363–371

    Article  CAS  Google Scholar 

  • Kunz J, Wilson MP, Kisseleva M, Hurley JH, Majerus PW, Anderson RA (2000) The activation loop of phosphatidylinositol phosphate kinases determines signaling specificity. Mol Cell 5:1–11

    Article  CAS  PubMed  Google Scholar 

  • Kuo CH, Kissinger JC (2008) Consistent and contrasting properties of lineage-specific genes in the apicomplexan parasites Plasmodium and Theileria. BMC Evol Biol. doi:10.1186/1471-2148-8-108

    PubMed  Google Scholar 

  • Kuo CH, Wares JP, Kissinger JC (2008) The Apicomplexan whole-genome phylogeny: an analysis of incongruence among gene trees. Mol Biol Evol 25:2689–2698

    Article  PubMed  Google Scholar 

  • Lang-Unnasch N, Reith ME, Munholland J, Barta JR (1998) Plastids are widespread and ancient in parasites of the phylum Apicomplexa. Int J Parasitol 28:1743–1754

    Article  CAS  PubMed  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) ClustalW and ClustalX version 2. Bioinformatics 23:2947–2948

    Article  CAS  PubMed  Google Scholar 

  • Leander BS, Clopton RE, Keeling PJ (2003) Phylogeny of gregarines (Apicomplexa) as inferred from small-subunit rDNA and β-tubulin. Int J Syst Evol Microbiol 53:345–354

    Article  CAS  PubMed  Google Scholar 

  • Leber W, Skippen A, Fivelman QL, Bowyer PW, Cockcroft S, Baker DA (2009) A unique phosphatidylinositol 4-phosphate 5-kinase is activated by ADP-ribosylation factor in Plasmodium falciparum. Int J Parasitol 39:645–653

    Article  CAS  PubMed  Google Scholar 

  • Le Hir H, Nott A, Moore MJ (2003) How introns influence and enhance eukaryotic gene expression. Trends Biochem Sci 28:215–220

    Article  PubMed  Google Scholar 

  • Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189

    Article  CAS  PubMed  Google Scholar 

  • Lien YY, Sheu SC, Liu HJ, Chen SC, Tsai MY, Luo SC, Wu KC, Liu SS, Su HY (2007) Cloning and nucleotide sequencing of the second internal transcribed spacer of ribosomal DNA for three species of Eimeria from chickens in Taiwan. Vet J 173:184–189

    Article  CAS  PubMed  Google Scholar 

  • Ling KH, Loo SS, Rosli R, Shamsudin MN, Mohamed R, Wan KL (2007a) In silico identification and characterization of a putative phosphatidylinositol 4-phosphate 5-kinase (PIP5K) gene in Eimeria tenella. In Silico Biol 7:115–121

    CAS  PubMed  Google Scholar 

  • Ling KH, Rajandream MA, Rivailler P, Ivens A, Yap SJ, Madeira AMBN, Mungall K, Billington K, Yee WY, Bankier AT, Carroll F, Durham AM, Peters N, Loo SS, Mat-Isa MN, Novaes J, Quail M, Rosli R, Mariana NS, Sobreira TJP, Tivey A, Wai SF, White S, Wu X, Kerhornou A, Blake D, Mohamed R, Shirley M, Gruber A, Berriman M, Tomley F, Dear PH and Wan KL (2007b) Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization. Genome Research 17:311–319

    Article  CAS  PubMed  Google Scholar 

  • Loijens JC, Anderson RA (1996) Type I phosphatidylinositol-4-phosphate-5 kinases are distinct members of this novel lipid kinase family. J Biol Chem 271:32937–32943

    Article  CAS  PubMed  Google Scholar 

  • Lovett JL, Sibley LD (2003) Intracellular calcium stores in Toxoplasma gondii govern invasion of host cells. J Cell Sci 116:3009–3016

    Article  CAS  PubMed  Google Scholar 

  • Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki C, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH (2007) CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res 35:D237–D240

    Article  CAS  PubMed  Google Scholar 

  • Nene V, Bishop R, Morzaria S, Gardner MJ, Sugimoto C, ole-MoiYoi OK, Fraser CM, Irvin A (2000) Theileria parva genomics reveals an atypical apicomplexan genome. Int J Parasitol 30:465–474

    Article  CAS  PubMed  Google Scholar 

  • Pasamontes L, Hug D, Humbelin M, Weber G (1993) Sequence of a major Eimeria maxima antigen homologous to the Eimeria tenella microneme protein Etp100. Mol Biochem Parasitol 57:171–174

    Article  CAS  PubMed  Google Scholar 

  • Periz J, Ryan R, Blake DP, Tomley FM (2009) Eimeria tenella microneme protein EtMIC4: capture of the full-length transcribed sequence and comparison with other microneme proteins. Parasitol Res 104:717–721

    Article  PubMed  Google Scholar 

  • Plattner F, Yarovinsky F, Romero S, Didry D, Carlier MF, Sher A, Soldati-Favre D (2008) Toxoplasma profilin is essential for host cell invasion and TLR11-dependent induction of an interleukin-12 response. Cell Host & Microbe 3:77–87

    Article  CAS  Google Scholar 

  • Riordan CE, Langreth SG, Sanchez LB, Kayser O, Keithly JS (1999) Preliminary evidence for a mitochondrion in Cryptosporidium parvum: phylogenetic and therapeutic implications. J Eukaryot Microbiol 46:52S–55S

    CAS  PubMed  Google Scholar 

  • Roy SW, Hartl DL (2006) Very little intron loss/gain in Plasmodium: Intron loss/gain mutation rates and intron number. Genome Res 16:750–756

    Article  CAS  PubMed  Google Scholar 

  • Roy SW, Penny D (2006) Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution. Genome Res 16:1270–1275

    Article  CAS  PubMed  Google Scholar 

  • Roy SW, Penny D (2007) Widespread intron loss suggests retrotransposon activity in ancient apicomplexans. Mol Biol Evol 14:1926–1933

    Article  Google Scholar 

  • Roy SW, Irimia M (2008) Mystery of intron gain: new data and new models. Trends Genet 25:67–73

    Article  PubMed  Google Scholar 

  • Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B (2000) Artemis: sequence visualization and annotation. Bioinformatics 16:944–945

    Article  CAS  PubMed  Google Scholar 

  • Sakharkar KR, Dhar PK, Chow VT (2004) Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis. Int J Syst Evol Microbiol 54:1937–1941

    Article  CAS  PubMed  Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  • Seeber F (1997) Consensus sequence of translational initiation sites from Toxoplasma gondii genes. Parasitol Res 83:309–311

    Article  CAS  PubMed  Google Scholar 

  • Shirley MW, Blake DP, White SE, Sheriff R, Smith AL (2004a) Integrating genetics and genomics to identify new leads for the control of Eimeria spp. Parasitol 128:S33–S42

    CAS  Google Scholar 

  • Shirley MW, Ivens A, Gruber A, Madeira AM, Wan K-L, Dear PH, Tomley FM (2004b) The Eimeria genome projects: a sequence of events. Trends Parasitol 20:199–201

    Article  CAS  PubMed  Google Scholar 

  • Shirley MW, Smith AL, Tomley FM (2005) The biology of avian Eimeria with an emphasis on their control by vaccination. Adv Parasitol 60:285–330

    Article  PubMed  Google Scholar 

  • Shirley MW, Smith AL, Blake DP (2007) Challenges in the successful control of the avian coccidia. Vaccine 25:5540–5547

    Article  CAS  PubMed  Google Scholar 

  • Soldati D, Foth BJ, Cowman AF (2004) Molecular and functional aspects of parasite invasion. Trends Parasitol 20:567–572

    Article  CAS  PubMed  Google Scholar 

  • Stanke M, Diekhans M, Baertsch R, Haussler D (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24:637–644

    Article  CAS  PubMed  Google Scholar 

  • Su YC, Fei ACY, Tsai FM (2003) Differential diagnosis of five avian Eimeria species by polymerase chain reaction using primers derived from the internal transcribed spacer (ITS-1) sequence. Vet Parasitol 117:221–227

    Article  CAS  PubMed  Google Scholar 

  • Tolias KF, Rameh LE, Ishihara H, Shibasaki Y, Chen J, Prestwich GD, Cantley LC, Carpenter CL (1998) Type I phosphatidylinositol-4-phosphate 5 kinases synthesizes the novel lipids phosphatidylinositol 3, 5-bisphosphate and phosphatidylinositol 5-phosphate. J Biol Chem 273:18040–18046

    Article  CAS  PubMed  Google Scholar 

  • Tomley FM, Clarke LE, Kawazoe U, Dijkema R, Kok JJ (1991) Sequence of the gene encoding an immunodominant microneme protein of Eimeria tenella. Mol Biochem Parasitol 49:277–288

    Article  CAS  PubMed  Google Scholar 

  • Vinogradov AE (2001) Intron length and codon usage. J Mol Evol 52:2–5

    CAS  PubMed  Google Scholar 

  • Yeh RF, Lim LP, Burge CB (2001) Computational inference of homologous gene structures in the human genome. Genome Res 11:803–816

    Article  CAS  PubMed  Google Scholar 

  • Zhang MQ (2002) Computational prediction of eukaryotic protein-coding genes. Nat Rev Genet 3:698–709

    Article  CAS  PubMed  Google Scholar 

  • Zhu G, Keithly JS, Philippe H (2000a) What is the phylogenetic position of Cryptosporidium? Int J Syst Evol Microbiol 50:1673–1681

    CAS  PubMed  Google Scholar 

  • Zhu G, Marchewka MJ, Keithly JS (2000b) Cryptosporidium parvum appears to lack a plastid genome. Microbiol 146:315–321

    CAS  Google Scholar 

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Acknowledgements

This project was supported by the Genomics and Molecular Biology Initiatives Programme of the Malaysia Genome Institute, Ministry of Science, Technology and Innovation Malaysia (Project No. 07-05-16-MGI-GMB10) and the Biotechnology and Biological Sciences Research Council, UK (BBSRC Grant BBE01089X1). The authors would like to acknowledge Dr Michael Quail for construction of the E. maxima BAC library and Karen Billington for construction of the SMART cDNA library. The authors would like to thank the Sanger Institute and the E. tenella Genome Consortium (http://www.sanger.ac.uk/Projects/E_tenella/consortium.shtml) for generation of the E. tenella sequencing data supported by the BBSRC and the Wellcome Trust.

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Correspondence to Beng-Kah Song.

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Goh, MY., Pan, MZ., Blake, D.P. et al. Eimeria maxima phosphatidylinositol 4-phosphate 5-kinase: locus sequencing, characterization, and cross-phylum comparison. Parasitol Res 108, 611–620 (2011). https://doi.org/10.1007/s00436-010-2104-7

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